L498 Thermolysin: Difference between revisions
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=Discovery of data collection parameters= | =Discovery of data collection parameters= | ||
Log in to pslogin.slac.stanford.edu, and then to psana. Carry through flags so that X-windows will work | |||
ssh -YAC $USER@pslogin.slac.stanford.edu | |||
ssh -YAC psana | |||
Go in to the working directory and source the package manager: | |||
cd ~/myrelease | |||
sit_setup | |||
Create a subdirectory for the 2014 tutorial files if not already done: | |||
mkdir -p cxi84914 | |||
List out the thermolysin XTC files: | |||
ls /reg/d/psdm/cxi/cxi84914/xtc/e157 | |||
Grab this configuration file: mkdark.cfg and put it in your cxi84914 directory | |||
=Prepare to mask out the untrusted pixels= | =Prepare to mask out the untrusted pixels= | ||
=Correct the detector metrology= | =Correct the detector metrology= | ||
Revision as of 22:55, 18 August 2014
In this tutorial, we assume that we are handed an SFX dataset containing thermolysin diffraction, but are not told anything else. We will have to go through all the data runs, figure out which one is to be used for dark subtraction, and account for untrusted pixels and detector metrology. At this point, we will be prepared to integrate and merge the data. Finally, we will perform simple molecular replacement and ask whether there is any Zn signal in the anomalous difference Fourier.
Discovery of data collection parameters
Log in to pslogin.slac.stanford.edu, and then to psana. Carry through flags so that X-windows will work
ssh -YAC $USER@pslogin.slac.stanford.edu ssh -YAC psana
Go in to the working directory and source the package manager:
cd ~/myrelease sit_setup
Create a subdirectory for the 2014 tutorial files if not already done:
mkdir -p cxi84914
List out the thermolysin XTC files:
ls /reg/d/psdm/cxi/cxi84914/xtc/e157
Grab this configuration file: mkdark.cfg and put it in your cxi84914 directory